On 2/15/18 12:38 PM, Poncho Arvayo Zatarain wrote:
Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in
vmd, is inverted, the water is in the middle and the lipid tails are outside.
How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s
file.tpr -n index -o file.gro -pbc whole but nothing happens. In index i use
option System. What can i do to flip the bilayer? should i use lipid and water
options in index?
Use the -trans option on the lipids to set a translation equal to half
the box along the membrane normal.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
